A novel method for in silico assessment of Methionine oxidation risk in monoclonal antibodies: Improvement over the 2-shell model

Davide Tavella; David R. Ouellette; Raffaella Garofalo; Kai Zhu; Jianwen Xu; Eliud O. Oloo; Christopher Negron; Peter M. Ihnat

doi:10.1371/journal.pone.0279689

Peer Review History

Original SubmissionJune 6, 2022
31 Aug 2022 Decision Letter - Ioscani Jimenez del Val, Editor PONE-D-22-16362A novel method for in silico assessment of Methionine oxidation risk in monoclonal antibodies: improvement over the 2-shell model.PLOS ONE Dear Dr. Tavella, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Oct 15 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Thank you for stating the following financial disclosure: “The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication. Davide Tavella, Christopher Negron, David R. Ouellette, Raffaella Garofalo and Jianwen Xu are employees of AbbVie and own AbbVie stock. Peter M. Ihnat was an employee of AbbVie at the time of this study. . Desmond, Prime, Maestro and BioLuminate are products sold by Schrodinger, Inc. Eliud O. Oloo and Kai Zhu performed this research as employees of Schrödinger, Inc.” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. 6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: No ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The solvent-accessible surface area (SASA) of the methionine side chain from a predicted antibody structure is a commonly used parameter to predict oxidation propensity of methionine residues in mAbs. Here Tavella and report an improved algorithm to predict methionine oxidation propensity (eg for partially buried Met). The algorithm considers not only the water molecules surrounding the methionine side chain, but also other residues side chains containing hydroxyl groups. The data are convicing (prediction vs forced degraded mAbs and ADCs), the manuscript is well written and of interest for the increasing stakeholders in antibody-based drugs. Altogether, the paper deserves to be published in PLOS One. Reviewer #2: The article on Met oxidation of MAbs is lucid and interesting. I endorse its ultimate publication as a good contribution to our understanding adventitious met oxidation, both in therapeutic molecules and in the cell. While I understand the focus on go/no go criteria to drive pharma decisions, well supported with the confusion matrices, I'd prefer some explicit statistical predictions of "oxidation riak" shall we say. Reporting a binary cutoff at a 15%? threshold is nice but why is that the right number? Cna the authors share mnre results from their calculations or present them in an alternate way, even as supporting material? A second point concerns MS data, will the new generated be made available in PRIDE or other database? This is important to the study's impact. Lastly I'm wondering about timescales. For calculating time averaged surface excursions of partially buried Met, and thinking about chemical reaction dynamics, what % of Met are available for chemical reaction at any time? Does this fit with the concentrations and reactivity of the oxidation agents used? ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0279689.r001
Revision 1
19 Nov 2022 Author Response Responses to editor’s comments: 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf We have corrected the format of the authors’ affiliation as per template instructions. We have changed the style and font size of sections’ and subsections’ titles. We have moved the captions of all figures at the end of the sections where they have been firstly referred to, and we have adjusted the captions’ style. We have moved all tables at the end of the sections where they have been firstly referred to. We have attached to this submission all the figures as separated files named accordingly to the style templates. Figures have been assessed by PACE. We hope that it now fits the style requirements, as described in the referred templates. 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. We have changed the “Disclosure” section in order to include the sources of funding for the work included in this submission. No grants were awarded to any authors. All authors participated to this work as employees of AbbVie or Schrödinger, and AbbVie sponsored and funded the study. 3. Thank you for stating the following financial disclosure: “The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication. Davide Tavella, Christopher Negron, David R. Ouellette, Raffaella Garofalo and Jianwen Xu are employees of AbbVie and own AbbVie stock. Peter M. Ihnat was an employee of AbbVie at the time of this study. . Desmond, Prime, Maestro and BioLuminate are products sold by Schrodinger, Inc. Eliud O. Oloo and Kai Zhu performed this research as employees of Schrödinger, Inc.” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. We have changed the “Disclosure” section as follow: AbbVie sponsored and funded the study, contributed to the design, participated in the collection, analysis, and interpretation of data, and in writing, reviewing, and approval of the final publication. Davide Tavella, Christopher Negron, David R. Ouellette, Raffaella Garofalo and Jianwen Xu are employees of AbbVie and may own AbbVie stock. Peter M. Ihnat was an employee of AbbVie at the time of this study. Desmond, Prime, Maestro and BioLuminate are products sold by Schrödinger, Inc. Schrödinger, Inc. provided support in the form of salary for authors Eliud O. Oloo and Kai Zhu but did not have any additional role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. The specific roles of these authors are articulated in the “author contributions”. The roles of the two funders, AbbVie and Schrödinger, have been explicitly stated as per provided instructions. 4. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. In this work, we have used two experimental datasets to validate the in silico predictions of methionine oxidation propensities and to reach the conclusions drawn in the manuscript. The first dataset, referred to in the manuscript as “clinical stage therapeutic (CST) antibodies dataset”, was derived from existing data, which are openly available at https://doi.org/10.1080/19420862.2017.1290753. This is the largest dataset used in this work, counting 14 antibodies and a total of 46 methionines. The second dataset, referred to in the manuscript as “internal dataset”, is derived from antibodies and ADCs currently in development at AbbVie. Therefore, due to its proprietary nature, supporting data cannot be made openly available. This is the smallest dataset used in this work, counting 7 antibodies and 2 ADCs for a total of 26 methionines. We want to highlight that the conclusions drawn from both datasets are in total agreement and the “internal dataset” serves as a further validation of the methods described in the manuscript. Moreover, in the supporting information S2 Table and S3 Table, we have disclosed more details regarding the calculations derived from the molecular dynamics simulations for both datasets. 5. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. We have added captions for Supporting Information Tables and Figures at the end of the manuscript. 6. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. We have revised the reference list to match the style and format of the journal. We have included a new reference (reference 49 in the final version). No retracted articles are referenced in the manuscript. Responses to reviewer #2: Reviewer #2: The article on Met oxidation of MAbs is lucid and interesting. I endorse its ultimate publication as a good contribution to our understanding adventitious met oxidation, both in therapeutic molecules and in the cell. While I understand the focus on go/no go criteria to drive pharma decisions, well supported with the confusion matrices, I'd prefer some explicit statistical predictions of "oxidation riak" shall we say. Reporting a binary cutoff at a 15%? threshold is nice but why is that the right number? Cna the authors share mnre results from their calculations or present them in an alternate way, even as supporting material? We agree with the reviewer’s points, and thus we included a statistical analysis of the linear correlation between experimentally measured oxidation levels of methionines and parameters calculated from the molecular dynamics simulations, specifically water coordination number and SASA. These results are reported in the modified S1 Fig and discussed in the result section at lines 443-450. The statistical analysis includes R-squared, correlation coefficient and Spearman correlation coefficient. The choice of 15% threshold is now discussed in the result section at line 281-282. We added 2 tables, S2 Table and S3 Table in supporting information, with details of the calculations from the molecular dynamics simulations. A second point concerns MS data, will the new generated be made available in PRIDE or other database? This is important to the study's impact. As discussed in the response to Editor’s comment #4, the dataset indicated as “internal dataset” is derived from antibodies and ADCs currently in development at AbbVie. Therefore, due to its proprietary nature, supporting data cannot be made openly available. The “clinical stage therapeutic (CST) antibodies dataset” was derived from existing data, which are openly available at https://doi.org/10.1080/19420862.2017.1290753. Lastly I'm wondering about timescales. For calculating time averaged surface excursions of partially buried Met, and thinking about chemical reaction dynamics, what % of Met are available for chemical reaction at any time? Does this fit with the concentrations and reactivity of the oxidation agents used? We have added a paragraph that address the different time scales involved in the molecular dynamics simulations and the kinetics of the oxidation reaction in the Discussion section at lines 514-525. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0279689.r002
13 Dec 2022 Decision Letter - Ioscani Jimenez del Val, Editor A novel method for in silico assessment of Methionine oxidation risk in monoclonal antibodies: improvement over the 2-shell model. PONE-D-22-16362R1 Dear Dr. Tavella, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Ioscani Jimenez del Val, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): Thank you for addressing all reviewer comments/suggestions. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Alain Beck ******** https://doi.org/10.1371/journal.pone.0279689.r003
Formally Accepted
19 Dec 2022 Acceptance Letter - Ioscani Jimenez del Val, Editor PONE-D-22-16362R1 A novel method for in silico assessment of Methionine oxidation risk in monoclonal antibodies: improvement over the 2-shell model. Dear Dr. Tavella: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Ioscani Jimenez del Val Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0279689.r004

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